Recent publications

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    1. Veetil, A.T., Jani, M., and Krishnan, Y.* (2018) Chemical control over membrane-initiated steroid signaling with a DNA nanocapsule. Proc. Natl. Acad. Sci. U.S.A.,  doi/10.1073/pnas.1712792115
    2. Devany J., Chakraborty, K. and Krishnan, Y.* (2018) Sub-cellular nanorheology reveals lysosomal viscosity as a reporter for lysosomal storage diseases. Nano Lett.,  DOI: 10.1021/acs.nanolett.7b05040
    3. Chakraborty, S. and Krishnan, Y.* (2017) A structural map of oncomiR-1 at single-nucleotide resolution Nucleic Acids Research, 45, 9694–9705
    4. Chakraborty, K., Leung, K., and Krishnan, Y.* (2017) High lumenal chloride in the lysosome is critical for lysosome function. eLife, 6, e28862
    5. Veetil, A.T., Chakraborty, K.,† Xiao, K.,† Minter, R. M.,† Sisodia, S. S., and Krishnan, Y.* (2017) Cell targetable DNA nanocapsules for spatiotemporal release of caged bioactive small molecules. Nature Nanotechnology, 12, 1183–1189 († equal contributions)
    6. Patel, A., Malinovska, L., Saha, S., Wang, J., Alberti, S., Krishnan, Y.* and Hyman, A.A.* (2017) ATP as a biological hydrotrope. Science, 356, 753–756.
    7. Joshi, H., Bhatia, D., Krishnan, Y. and Maiti, P.K.* (2017) Probing the Structure and in Silico Stability of Cargo Loaded DNA Icosahedron using MD Simulations Nanoscale, 9, 4467–4477
    8. Bhatia, D., Arumugam, S., Nasilowski, M., Joshi, H., Wunder, C., Chambon, V., Prakash, V., Grazon, C., Nadal, B., Maiti, P. K., Johannes, L.*, Dubertret, B.* and Krishnan, Y.* (2016) Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways. Nature Nanotechnology, 11, 1112–1119
    9. Chakraborty, K., Veetil, A. T., Jaffrey, S. R.*, and Krishnan, Y.* (2016) Nucleic Acid–Based Nanodevices in Biological Imaging. Annual Reviews of Biochemistry, 85, 349–373
    10. Prakash, V.,† Saha, S.,† Chakraborty, K. and Krishnan, Y.* (2016) Rational design of a quantitative, pH-insensitive, nucleic acid based fluorescent chloride reporter. Chemical Science, 7, 1946–1953 († both authors have contributed equally)
    11. Saha, S., Prakash, V., Halder, S., Chakraborty, K. and Krishnan, Y.* (2015) A pH-independent DNA nanodevice for quantifying chloride transport in organelles of living cells Nature Nanotechnology, 10, 645–651
    12. Surana, S., Shenoy, A. R.* and Krishnan, Y.* (2015) Designing DNA nanodevices for compatibility with the immune system of higher organisms. Nature Nanotechnology, 10, 741–747
      1. Complete list of Publications

        1. Nucleic acid nano-devices in live imaging
        2. Nucleic acid structure and dynamics
        3. Naturally occurring nucleic acid nano-devices
        4. Reviews and commentaries
        5. Patents
        6. Nucleic acid nano-devices in live imaging

          1. Veetil, A.T., Jani, M., and Krishnan, Y.* (2018) Chemical control over membrane-initiated steroid signaling with a DNA nanocapsule. Proc. Natl. Acad. Sci. U.S.A.,  doi/10.1073/pnas.1712792115
          2. Devany J., Chakraborty, K. and Krishnan, Y.* (2018) Sub-cellular nanorheology reveals lysosomal viscosity as a reporter for lysosomal storage diseases. Nano Lett.,  DOI: 10.1021/acs.nanolett.7b05040
          3. Chakraborty, K., Leung, K., and Krishnan, Y.* (2017) High lumenal chloride in the lysosome is critical for lysosome function. eLife, 6, e28862.
          4. Veetil, A.T., Chakraborty, K.,† Xiao, K.,† Minter, R. M.,† Sisodia, S. S., and Krishnan, Y.* (2017) Cell targetable DNA nanocapsules for spatiotemporal release of caged bioactive small molecules. Nature Nanotechnology,  12, 1183–1189 († equal contributions)
          5. Bhatia, D., Arumugam, S., Nasilowski, M., Joshi, H., Wunder, C., Chambon, V., Prakash, V., Grazon, C., Nadal, B., Maiti, P. K., Johannes, L.*, Dubertret, B.* and Krishnan, Y.* (2016) Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways. Nature Nanotechnology, 11, 1112–1119
          6. Chakraborty, K., Veetil, A. T., Jaffrey, S. R.*, and Krishnan, Y.* (2016) Nucleic Acid–Based Nanodevices in Biological Imaging. Annual Reviews of Biochemistry, 85, 349–373
          7. Prakash, V.,† Saha, S.,† Chakraborty, K. and Krishnan, Y.* (2016) Rational design of a quantitative, pH-insensitive, nucleic acid based fluorescent chloride reporter. Chemical Science, 7, 1946–1953. († both authors have contributed equally)
          8. Surana, S., Shenoy, A. R.* and Krishnan, Y.* (2015) Designing DNA nanodevices for compatibility with the immune system of higher organisms. Nature Nanotechnology, 10, 741–747
          9. Saha, S., Prakash, V., Halder, S., Chakraborty, K. and Krishnan, Y.* (2015) A pH-independent DNA nanodevice for quantifying chloride transport in organelles of living cells Nature Nanotechnology, 10, 645–651
          10. Banerjee, A., Grazon, C., Nadal, B., Pons, T., Krishnan, Y. and Dubertret, B. * (2015) Fast, efficient and stable conjugation of multiple DNA strands on colloidal quantum dots Bioconjugate Chem., 26, 1582–1589
          11. Modi, S., Halder, S., Nizak, C. and Krishnan, Y.* (2014) Recombinant antibody mediated delivery of organelle-specific DNA pH sensors along endocytic pathways. Nanoscale, 6, 1144–1152
          12. Ganesh, K.N. and Krishnan Y. (2013) Nucleic Acids - Chemistry and Applications. J. Org. Chem. 78, 12283–12287.
          13. Modi, S., Nizak, C., Surana, S., Halder, S. and Krishnan, Y*. (2013)Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell. Nature Nanotechnology, 8, 459–467
          14. Surana, S., Bhatia, D. and Krishnan, Y.* (2013) A method to study in vivo stability of DNA nanostructures. Methods, 64, 94–100.
          15. Surana, S. and Krishnan, Y.* (2013) A method to map spatiotemporal pH changes in a multicellular living organism using a DNA nanosensor. Methods Mol. Biol. 991, 9–23
          16. Krishnan, Y.*, Bathe, M.* (2012) Designer nucleic acids to probe and program the cell.Trends in Cell Biology, 22, 624–633
          17. Modi, S. and Krishnan, Y.* (2011) A method to map spatiotemporal pH changes insde living cells using a pH triggered DNA nanoswitch. Methods Mol. Biol. 749, 61–77.
          18. Surana, S., Bhat, J.M., Koushika, S.P. and Krishnan, Y.* (2011) An autonomous DNA nanomachine maps spatiotemporal pH changes in a molticellolar living organism.Nature Communications, 2, 340
          19. Bhatia, D., Surana, S., Chakraborty, S., Koushika, S.P. and Krishnan, Y.* (2011) A synthetic, icosahedral DNA-based host-cargo complex for functional in vivo imaging.Nature Communications, 2, 339
          20. Modi, S., Swetha, M. G., Goswami, D., Gupta, G. D., Mayor, S., Krishnan, Y.* (2009) A DNA nanomachine maps spatiotemporal pH changes in living cells. Nature Nanotechnology, 4, 325–330

        Nucleic acid structure and dynamics

        1. Patel, A., Malinovska, L., Saha, S., Wang, J., Alberti, S., Krishnan, Y.* and Hyman, A.A.* (2017) ATP as a biological hydrotrope. Science, 356, 753–756
        2. Joshi, H., Bhatia, D., Krishnan, Y. and Maiti, P.K.* (2017) Probing the Structure and in Silico Stability of Cargo Loaded DNA Icosahedron using MD Simulations Nanoscale, 9, 4467–4477
        3. Halder, S. and Krishnan, Y.* (2015) Design of ultrasensitive DNA-based fluorescent pH sensitive nanodevices. Nanoscale, 7, 10008–10012
        4. Lannes, L., Halder, S., Krishnan, Y. and Schwalbe, H.* (2015) Tuning the pH Response of i-Motif DNA Oligonucleotides ChemBioChem, 16, 1647–1656
        5. Chakraborty, S., Mehtab, S. and Krishnan, Y.* (2014) The predictive power of synthetic nucleic acid technologies in RNA biology. Acc. Chem. Res. 47, 1710–1719
        6. Sharma, S., Zaveri, A., Visweswariah, S.S and Krishnan, Y.* (2014) A fluorescent nucleic acid-based nanodevice quantitatively images elevated cAMP in membrane bound compartments. Small, 10, 4276–4280
        7. Banerjee, A., Bhatia, D., Saminathan, A., Chakraborty, S., Kar, S. and Krishnan, Y.* (2013) Controlled release of encapsulated cargo from a DNA icosahedron using a chemical trigger. Angew. Chem. Int. Ed. 52, 6854–6857
        8. Bhatia, D., Chakraborty, S., Mehtab, S. and Krishnan, Y.* (2013) A method to encapsulate molecular cargo within DNA icosahedra. Methods Mol. Biol. 991, 65–80
        9. Bhatia, D. and Krishnan, Y. (2013) Designer nucleic acid-based devices in nanomedicine. In Erdmann, V.A., Barcisjewski, J. (eds), DNA and RNA Nanobiotechnologies in Medicine: Diagnosis and Treatment of Diseases. pp 1–10
        10. Saha, S. and Krishnan, Y. (2012) pH sensitive DNA devices. In Fox, K.R., Brown, T (ed), DNA Conjugates and Sensors. Royal Society of Chemistry publishing, Cambridge, pp166–183
        11. Saha, S., Chakraborty, K. and Krishnan, Y*. (2012) Tunable, colorimetric DNA based pH sensors mediated by A-motif formation. Chem. Commun. 48, 2513–2515
        12. Bhatia, D., Sharma, S. and Krishnan, Y*. (2011) Synthetic, biofunctional nucleic acid-based molecular devices. Curr Opin Biotechnol, 22, 475–484
        13. Krishnan, Y and Simmel, F. C. (2011) Nucleic Acid Based Molecular Devices. Angew. Chem. Int. Ed. 50, 3124–3156
        14. Modi, S., Bhatia, D., Simmel, F. C., Krishnan, Y.* (2010) Structural DNA Nanotechnology: From bases to bricks, from structure to function. J. Phys. Chem. Lett. 1, 1999–2005
        15. Saha, S., Bhatia, D., Krishnan, Y.* (2010) pH toggled DNA architectures: Reversible assembly of a 3WJ into extended 1D architectures through A-motif formation . Small, 6, 1288–1292
        16. Chakraborty, S., Sharma, S., Maiti, P. K., Krishnan, Y.* (2009) The poly dA helix: A new structural motif for high-performance DNA-based molecular switches . Nucleic Acids Res. 37, 2810-2817
        17. Bhatia, D., Mehtab, S., Krishnan, R., Indi, S.S., Basu, A., Krishnan, Y.*(2009)Icosahedral DNA nanocapsules via modular assembly. Angew. Chem. Int. Ed. 48, 4134–4137. (featured on journal frontispiece)
        18. Paol,  A.; Sengupta, P.;  Krishnan, Y.; Ladame, S.* (2008) Combining G-quadruplex targeting motifs on a single PNA scaffold: hybrid (3+1) PNA-DNA bimolecular quadruplex. Chem.Eur.J. 14, 8682-8689
        19. Chakraborty, S.; Krishnan, Y.* (2008) Kinetic Hybrid i-motifs: Intercepting DNA with RNA to form a DNA2-RNA2 i-motif. Biochimie, 90, 1088–1095
        20. Chakraborty, S.; Modi, S.; Krishnan, Y.* (2008) The RNA2-PNA2 Hybrid I-motif - A novel RNA-based building block. Chem. Commun., 70–72
        21. Ghodke, H. B.; Krishnan, R.; Vignesh, K.; Kumar, G.V.P.; Narayana, C.; Krishnan, Y.* (2007) The I-tetraplex building block: Rational Design and Controlled Fabrication of robust 1D DNA Scaffolds via non-Watson Crick self assembly. Angew. Chem. Int. Ed., 46, 2646–2649
        22. Gavory, G.; Symmons, M. F.; Krishnan-Ghosh, Y.;Klenerman, D.; Balasubramanian, S.* (2006) Structural Analysis of the Catalytic Core of Human Telomerase RNA by FRETand Molecolar Modeling. Biochemistry, 45, 13304–13311
        23. Modi, S., Wani, A. H., Krishnan, Y.* (2006) The PNA-DNA hybrid I-motif - Implications for sugar-sugar contacts in i-motif tetramerization. Nucleic Acids Research, 34, 4353–4363
        24. Krishnan-Ghosh, Y.; Stephens, E.; Balasubramanian, S.*(2005) PNA forms an I-motif. Chem. Commun. 5278–5280
        25. Krishnan-Ghosh, Y.; Whitney, A. M.; Balasubramanian, S.* (2005)  Dynamic covalent chemistry on self-templating PNA oligomers: Formation of a bimolecolar PNA quadruplex. Chem. Commun., 3068–3070
        26. Krishnan-Ghosh, Y.; Liu, D.; Balasubramanian, S.* (2004) Formation of an interlocked quadruplex dimer by d(GGGT). J. Am. Chem. Soc. 126, 11009–11016
        27. Krishnan-Ghosh, Y.; Stephens, E.; Balasubramanian, S.* (2004)A PNA4 quadruplex.  J. Am. Chem. Soc.  126, 5944–5945
        28. Krishnan-Ghosh , Y.; Balasubramanian, S.* (2003) Dynamic covalent chemistry on self-templating peptides: Formation of a disolfide-linked beta-hairpin mimic. Angew. Chem. Int. Ed. 42, 2171–2173
        29. Ghosh Y. K.; Visweswariah, S. S.; Bhattacharya, S. * (2002) Advantage of the ether linkage between the positive charge and the cholesteryl skeleton in cholesterol-based amphiphiles as vectors for gene delivery. Bioconjugate Chem. 13, 378–384 
        30. Bhattacharya, S.*; Krishnan-Ghosh, Y. (2002) 2-Halooxyethylene ethers of cholesterol as novel single component, room temperature cholesteric LC materials.Mol. Cryst. Liq. Cryst. 381, 33-41 
        31. Wills, A. J.; Krishnan-Ghosh, Y.; Balasubramanian S.* (2002) Synthesis of a polymer-supported oxazolidine aldehyde for asymmetric chemistry. J. Org. Chem. 67, 6646-6652
        32. Horsey, I.; Krishnan-Ghosh, Y.; Balasubramanian, S. (2002) Enhanced cooperative binding of oligonucleotides to form DNA duplexes mediated by metal ion chelation Chem. Commun. 1950-1951 
        33. Bhattacharya, S.; Krishnan-Ghosh, Y. (2001) First report of phase selective gelation of oil from oil/water mixtures. Possible implications toward containing oil spills. Chem. Commun., 185–186
        34. Bhattacharya, S.; Krishnan-Ghosh, Y. (2001) Vesicle formation from oligo(oxyethylene)-bearing cholesteryl amphiphiles: Site-selective effects of oxyethylene units on the membrane order and thickness. Langmuir 17, 2067–2075
        35. Krishnan-Ghosh, Y.; Gopalan, R. S.; Kolkarni, G. U.; Bhattacharya, S. (2001) Structure of cholest-5-en-3 beta-oxy-5-bromopentane by single-crystal X-ray diffraction at 130 K. J. Mol. Structure 560, 345–355 
        36. Krishnan-Ghosh, Y.; Bhattacharya, S.* (2001) Membrane formation from oxyethylene bearing cationic cholesterol derivatives. Ind. J. Chem. B. 40, 891–894
        37. Krishnan-Ghosh, Y., Bhattacharya, S.* (2001) Thermal lipid order-disorder transitions in mixtures of cationic cholesteryl lipid analogues and dipalmitoyl phosphatidylcholine membranes. J. Phys. Chem. B. 105, 10257–10265
        38. Ghosh, Y.K., Visweswariah, S. S., Bhattacharya, S.* (2000) Nature of linkage between cationic headgroup and cholesteryl skeleton controls gene transfection efficiency .  FEBS Lett. 473, 341–344

        Naturally occurring nucleic acid nano-devices

        1. Chakraborty, S. and Krishnan, Y.* (2017) A structural map of oncomiR-1 at single-nucleotide resolution. Nucleic Acids Research, 2017, 45, 9694–9705
        2. Chakraborty, S., Mehtab, S. and Krishnan, Y.* (2014) The predictive power of synthetic nucleic acid technologies in RNA biology. Acc. Chem. Res. 47, 1710–1719
        3. Chakraborty, S., Mehtab, S., Patwardhan, A.R., Krishnan, Y.* (2012) Pri-miR-17-92a Transcript folds into a tertiary structure and autoregolates its processing. RNA 18, 1014–1028

        Reviews and commentaries:

        1. Voices of biotech   Nature Biotechnology, 34, (2016),  270–275
        2. Nature nanotechnology 10 the anniversary issue opinion piece  Nature Nanotechnology (2016) 11,  828–834
        3. Chakraborty, K., Veetil, A. T., Jaffrey, S. R.*, and Krishnan, Y.* (2016) Nucleic Acid–Based Nanodevices in Biological Imaging. Annual Reviews of Biochemistry, 85, 349–373
        4. Surana, S., Shenoy, A. R.* and Krishnan, Y.* (2015) Designing DNA nanodevices for compatibility with the immune system of higher organisms. Nature Nanotechnology, 10, 741–747
        5. Chakraborty, S., Mehtab, S. and Krishnan, Y.* (2014) The predictive power of synthetic nucleic acid technologies in RNA biology. Acc. Chem. Res. 47, 1710–1719
        6. Ghosh, A. and Krishnan, Y. (2014) At a long-awaited turning point. NatureNanotechnology, 9, 491–494
        7. Krishnan, Y., Bathe, M. (2012) Designer nucleic acids to probe and program the cell.Trends in Cell Biology, 22, 624–633
        8. Bhatia, D., Chakraborty, S. and Krishnan, Y.* (2012) Designer DNA give RNAi more spine. Nature Nanotechnology, 7, 344–346
        9. Krishnan, Y and Simmel, F. C. (2011) Nucleic Acid Based Molecolar Devices. Angew. Chem. Int. Ed. 50, 3124–3156
        10. Modi, S., Bhatia, D., Simmel, F. C., Krishnan, Y.* (2010) Structural DNA Nanotechnology: From bases to bricks, from structure to function. J.Phys. Chem. Lett. 1, 1999–2005
        11. Pitchiaya, S., Krishnan, Y.* (2006) First Blueprint, Now Bricks: DNA as construction material on the nanoscale. Chem. Soc. Rev., 35, 1111–1121

        Patents:

        1. Modular assembly of novel icosahedral DNA nanocapsules with encapsulating ability.

          Yamuna Krishnan. Under prosecution at USPTO.

        2. The A-motif: A pH trigger for hybridization of DNA strands

          Saikat Chakraborty and Yamuna Krishnan.
          US Patent granted July 10, 2012. USPTO no: 8216850.

        3. FRET based pH Sensor using nucleic acid assemblies.

          Yamuna Krishnan, Satyajit Mayor and Souvik Modi. Under prosecution at USPTO.

        4. An engineered nucleic acid assembly, vector, cell, methods and kit thereof

          Souvik Modi and Yamuna Krishnan. Complete IN and PCT filed.

        5. A process for encapsulating functional biomolecules and encapsulated product thereof.

          Dhiraj Bhatia and Yamuna Krishnan. Complete IN and PCT filed.
          Winner of the Amulya 2012 award from the Karnataka State Innovation Council.

        6. Nucleotide sequences, nucleic acid sensors and methods thereof.

          Suruchi Sharma and Yamuna Krishnan. Complete IN filed.

        7. Nucleic Acids based sensor and methods thereof.

          Sonali Saha and Yamuna Krishnan. Complete IN filed.

        8. A process for encapsulating functional biomolecules and encapsulated product thereof.

          Souvik Modi, Sunaina Surana and Yamuna Krishnan. PCT filed. PCT/IB/2014/059236